I'm not completely sure where to start. I currently have a setup for our local parade in which we have 32 strips of LED's with 15 leds each strip, these strips are laid vertically on our vehicle. We use a LED fx controller to sequence each strip on or off depending on the selected program ( with transistor boards) It takes a full day to install these leds and each home made magnetic strip needs periodic maintenance. ( I'm going to sell the whole lot)

Now for my current project:

I am switching to RGB 3528 and 5050 led stripsHave an Arduino mega and LED painter boardsSeveral meters of rgb led strips

Would like to control 2 X 16 strips via the led painter and arduino, similar to the ledfx controller and possibly music controlled.

Probably, if you have the source code, and if the program is written C (not the PIC assembly language).

But, all of the I/O is going to be different, the timing/delay will probably be different, and I'd guess that you'll have to modify about half of the lines in the code. So, it won't be much easier than starting-over. You might be able to get some hints & clues from the old software, but it's often easier to write and debug your own code rather than trying to make someone elses code work on a different system.

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Are there any programs similar to the one I would like to create?

I'm not sure what kind of patterns/sequencing you are doing or how many LEDs/channels that you can address. But, take a look at Blinkenlight Experiments. That should get you started.